Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002172.1 Hibiscus syriacus cultivar Beakdansim tig00004428_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 84475
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:3676 original size:75 final size:75
Alignment explanation
Indices: 3583--3733 Score: 284
Period size: 75 Copynumber: 2.0 Consensus size: 75
3573 CAGGTGCAGA
*
3583 TCCGGTCAGCTGATGAGCCAGCAACGACATTCTATCAGTGCTTGAAATGCGAGAAGATGTGGCGT
1 TCCGGTCAGCTGATGAGCCAGCAACGACATTCTATCAGTGCTTGAAATGCCAGAAGATGTGGCGT
3648 GAGGATTGAG
66 GAGGATTGAG
*
3658 TCCGGTCAGCTGATGAGCCAGCAATGACATTCTATCAGTGCTTGAAATGCCAGAAGATGTGGCGT
1 TCCGGTCAGCTGATGAGCCAGCAACGACATTCTATCAGTGCTTGAAATGCCAGAAGATGTGGCGT
3723 GAGGATTGAG
66 GAGGATTGAG
3733 T
1 T
3734 ACATGTTATC
Statistics
Matches: 74, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
75 74 1.00
ACGTcount: A:0.26, C:0.19, G:0.31, T:0.24
Consensus pattern (75 bp):
TCCGGTCAGCTGATGAGCCAGCAACGACATTCTATCAGTGCTTGAAATGCCAGAAGATGTGGCGT
GAGGATTGAG
Found at i:10416 original size:15 final size:15
Alignment explanation
Indices: 10376--10417 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 15
10366 TTAGGCACCA
* *
10376 AAACTTTCAATGTTT
1 AAACTTTCAATCTAT
*
10391 ACACTTT-AATCTAT
1 AAACTTTCAATCTAT
10405 AAACTTTCAATCT
1 AAACTTTCAATCT
10418 TTAGAATTTA
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
14 11 0.50
15 11 0.50
ACGTcount: A:0.36, C:0.19, G:0.02, T:0.43
Consensus pattern (15 bp):
AAACTTTCAATCTAT
Found at i:18608 original size:30 final size:30
Alignment explanation
Indices: 18573--18726 Score: 170
Period size: 30 Copynumber: 5.0 Consensus size: 30
18563 CTAGATCACC
*
18573 AAAGTTTGAAATTTGTAACATCAAGAACCA
1 AAAGTTTGAAATTTGTAACAACAAGAACCA
* **
18603 AAAGTTTTAAATTTGTAACAACACCAACCA
1 AAAGTTTGAAATTTGTAACAACAAGAACCA
18633 AAAGTTTGAAATTTGT---AACAAGAACCAA
1 AAAGTTTGAAATTTGTAACAACAAGAACC-A
*
18661 AAGTTTGAGATTTGAAATTTGCAACAACAAGAACCA
1 AA-----AG-TTTGAAATTTGTAACAACAAGAACCA
*
18697 AAAGTCTGAAATTTGTAACAACAAGAACCA
1 AAAGTTTGAAATTTGTAACAACAAGAACCA
18727 TAGATTCTAT
Statistics
Matches: 104, Mismatches: 10, Indels: 20
0.78 0.07 0.15
Matches are distributed among these distances:
27 8 0.08
28 3 0.03
30 65 0.62
31 2 0.02
33 2 0.02
34 11 0.11
36 3 0.03
37 10 0.10
ACGTcount: A:0.47, C:0.15, G:0.13, T:0.25
Consensus pattern (30 bp):
AAAGTTTGAAATTTGTAACAACAAGAACCA
Found at i:18680 original size:34 final size:35
Alignment explanation
Indices: 18637--18711 Score: 98
Period size: 37 Copynumber: 2.1 Consensus size: 35
18627 CAACCAAAAG
* * *
18637 TTTGAAATTTG-TAACAAGAACCAAAAGTTTGAGA
1 TTTGAAATTTGACAACAAGAACCAAAAGTCTGAAA
18671 TTTGAAATTTGCAACAACAAGAACCAAAAGTCTGAAA
1 TTTGAAATTTG--ACAACAAGAACCAAAAGTCTGAAA
18708 TTTG
1 TTTG
18712 TAACAACAAG
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
34 11 0.31
37 24 0.69
ACGTcount: A:0.44, C:0.12, G:0.16, T:0.28
Consensus pattern (35 bp):
TTTGAAATTTGACAACAAGAACCAAAAGTCTGAAA
Found at i:22557 original size:18 final size:19
Alignment explanation
Indices: 22532--22577 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 19
22522 TAATATTATT
22532 TTTATAATA-ATTTTAT-A
1 TTTATAATACATTTTATGA
22549 TTGTATAATATCATTTTATGA
1 TT-TATAATA-CATTTTATGA
22570 TTTATAAT
1 TTTATAAT
22578 CATAATGTAC
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
17 2 0.08
18 7 0.28
20 13 0.52
21 3 0.12
ACGTcount: A:0.37, C:0.02, G:0.04, T:0.57
Consensus pattern (19 bp):
TTTATAATACATTTTATGA
Found at i:22572 original size:64 final size:64
Alignment explanation
Indices: 22453--22574 Score: 151
Period size: 64 Copynumber: 1.9 Consensus size: 64
22443 CATTGATTAT
* ** * *
22453 TATGTTAATATTATTTTTATAAATATTTGTAGTTGTATTTTACCTTTTCTAGATTTATTATTGA
1 TATGTTAATATTATTTTTATAAATATTTGTAATTGTATAATACATTTTATAGATTTATTATTGA
22517 TATGTTAATATTATTTTTAT-AATAATTT-TATATTGTATAATATCATTTTAT-GATTTAT
1 TATGTTAATATTATTTTTATAAAT-ATTTGTA-ATTGTATAATA-CATTTTATAGATTTAT
22575 AATCATAATG
Statistics
Matches: 50, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
63 5 0.10
64 39 0.78
65 6 0.12
ACGTcount: A:0.31, C:0.03, G:0.07, T:0.58
Consensus pattern (64 bp):
TATGTTAATATTATTTTTATAAATATTTGTAATTGTATAATACATTTTATAGATTTATTATTGA
Found at i:23064 original size:29 final size:29
Alignment explanation
Indices: 23032--23139 Score: 83
Period size: 29 Copynumber: 3.7 Consensus size: 29
23022 TTATAATATT
* * * *
23032 TTAAAATTAATATAAAATATTTTTTATAG
1 TTAAAATTAAAATAAAATATATTTTAAAA
* * *
23061 TTAAGATAAAAATAAAACATATTTTAAAA
1 TTAAAATTAAAATAAAATATATTTTAAAA
* * ***
23090 TTAAAA-TAAGAATAAAATATAATATATTT
1 TTAAAATTAA-AATAAAATATATTTTAAAA
23119 TTAAAATATAAAATAAAATAT
1 TTAAAAT-TAAAATAAAATAT
23140 CTATATTTTC
Statistics
Matches: 61, Mismatches: 15, Indels: 5
0.75 0.19 0.06
Matches are distributed among these distances:
28 2 0.03
29 46 0.75
30 10 0.16
31 3 0.05
ACGTcount: A:0.58, C:0.01, G:0.03, T:0.38
Consensus pattern (29 bp):
TTAAAATTAAAATAAAATATATTTTAAAA
Found at i:23100 original size:34 final size:36
Alignment explanation
Indices: 23069--23138 Score: 101
Period size: 35 Copynumber: 2.0 Consensus size: 36
23059 AGTTAAGATA
23069 AAAATAAAACATA-TTTTAAAAT-TAAAATAAGAAT
1 AAAATAAAACATATTTTTAAAATATAAAATAAGAAT
* *
23103 AAAATATAATATATTTTTAAAATATAAAATAA-AAT
1 AAAATAAAACATATTTTTAAAATATAAAATAAGAAT
23138 A
1 A
23139 TCTATATTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
34 11 0.34
35 13 0.41
36 8 0.25
ACGTcount: A:0.64, C:0.01, G:0.01, T:0.33
Consensus pattern (36 bp):
AAAATAAAACATATTTTTAAAATATAAAATAAGAAT
Found at i:23144 original size:29 final size:29
Alignment explanation
Indices: 23090--23148 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 29
23080 TATTTTAAAA
*
23090 TTAAAATAAGAATAAAATATAATATATTT
1 TTAAAATAAAAATAAAATATAATATATTT
*
23119 TTAAAATATAAAATAAAATAT-CTATATTT
1 TTAAAATA-AAAATAAAATATAATATATTT
23148 T
1 T
23149 CAAGTTAAGA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
29 16 0.59
30 11 0.41
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.41
Consensus pattern (29 bp):
TTAAAATAAAAATAAAATATAATATATTT
Found at i:24439 original size:4 final size:4
Alignment explanation
Indices: 24432--24456 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
24422 ATATATAAAT
24432 ATAA ATAA ATAA ATAA ATAA ATAA A
1 ATAA ATAA ATAA ATAA ATAA ATAA A
24457 ATAGTATTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
ATAA
Found at i:29656 original size:3 final size:3
Alignment explanation
Indices: 29650--29735 Score: 82
Period size: 3 Copynumber: 28.7 Consensus size: 3
29640 ACTGTCATCA
* * * * * *
29650 TCG TCG TCA TCG TCG TCA TCA TCG TCG TCG TCG TCA TTG TCA TCG TCG
1 TCG TCG TCG TCG TCG TCG TCG TCG TCG TCG TCG TCG TCG TCG TCG TCG
* * * *
29698 TTG TCG TCG TCA CCA TCG TCG TCG TCG TCG TCG TCG TC
1 TCG TCG TCG TCG TCG TCG TCG TCG TCG TCG TCG TCG TC
29736 CTGAGCAGGT
Statistics
Matches: 67, Mismatches: 16, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
3 67 1.00
ACGTcount: A:0.08, C:0.33, G:0.24, T:0.35
Consensus pattern (3 bp):
TCG
Found at i:29669 original size:21 final size:21
Alignment explanation
Indices: 29643--29729 Score: 120
Period size: 21 Copynumber: 4.1 Consensus size: 21
29633 ACTCCTCACT
*
29643 GTCATCATCGTCGTCATCGTC
1 GTCATCATCGTCGTCGTCGTC
29664 GTCATCATCGTCGTCGTCGTC
1 GTCATCATCGTCGTCGTCGTC
* ** *
29685 ATTGTCATCGTCGTTGTCGTC
1 GTCATCATCGTCGTCGTCGTC
*
29706 GTCACCATCGTCGTCGTCGTC
1 GTCATCATCGTCGTCGTCGTC
29727 GTC
1 GTC
29730 GTCGTCCTGA
Statistics
Matches: 56, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 56 1.00
ACGTcount: A:0.10, C:0.32, G:0.23, T:0.34
Consensus pattern (21 bp):
GTCATCATCGTCGTCGTCGTC
Found at i:31748 original size:111 final size:111
Alignment explanation
Indices: 31608--31829 Score: 374
Period size: 111 Copynumber: 2.0 Consensus size: 111
31598 ATTACAAAAA
* * *
31608 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTA-TAAATAATTTAAATT
1 TTAATTCTTAATCTAATAATCATACATTAAATAAATCAACTAAATATTACT-AATAATATAAATT
*
31672 AAATTAAAACGTTAAAATGTTACCGTATCAACAAAGTGTCGAGATAT
65 AAATTAAAACGTTAAAATGTTACCGTATCAACAAAGTGTAGAGATAT
31719 TTAATTCTTAATCTAATAATCATACATTAAATAAATCAACTAAATATTACTAATAATATAAATTA
1 TTAATTCTTAATCTAATAATCATACATTAAATAAATCAACTAAATATTACTAATAATATAAATTA
* *
31784 AATTAAAACTTTAAAATGTTACCGTATCAGCAAAGTGTAGAGATAT
66 AATTAAAACGTTAAAATGTTACCGTATCAACAAAGTGTAGAGATAT
31830 ATGATTTCCA
Statistics
Matches: 104, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
111 103 0.99
112 1 0.01
ACGTcount: A:0.47, C:0.11, G:0.07, T:0.36
Consensus pattern (111 bp):
TTAATTCTTAATCTAATAATCATACATTAAATAAATCAACTAAATATTACTAATAATATAAATTA
AATTAAAACGTTAAAATGTTACCGTATCAACAAAGTGTAGAGATAT
Found at i:32169 original size:50 final size:50
Alignment explanation
Indices: 32094--32202 Score: 155
Period size: 50 Copynumber: 2.2 Consensus size: 50
32084 GATCCGCGCT
* * * *
32094 AGGGGGGCGCTATACCCACGTGGCGCCAGATCACCGTATATCGCGGGGCA
1 AGGGGCGCGCTATACCCACGTGGCGCCAAATCACCGTATAGCGCAGGGCA
* **
32144 AGGGGCGCGCTATACCCACGTGGCGCCAAATCAGCGTATAGCGCAGTTCA
1 AGGGGCGCGCTATACCCACGTGGCGCCAAATCACCGTATAGCGCAGGGCA
32194 AGGGGCGCG
1 AGGGGCGCG
32203 TTTTACTGCT
Statistics
Matches: 52, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
50 52 1.00
ACGTcount: A:0.21, C:0.29, G:0.36, T:0.14
Consensus pattern (50 bp):
AGGGGCGCGCTATACCCACGTGGCGCCAAATCACCGTATAGCGCAGGGCA
Found at i:32918 original size:112 final size:112
Alignment explanation
Indices: 32715--33396 Score: 991
Period size: 112 Copynumber: 6.1 Consensus size: 112
32705 TTGTCGGTTT
* * *
32715 GTGTCGATACTTTATAAAAATATATTGATCCATAATAATATAACAGGTAACAAAAATGACAAAAC
1 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAA-AAAAATGACAAAAC
* *
32780 CGGTCTATAAAAGACAAAATAGGTAAAGCGCTACCGGATATATTGAAA
65 CGGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
* * * *
32828 GTATTGATACTTTATAAAAATGTATCGATCCATAATAATATAACATGTAAAAAAATGACAAAACC
1 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACC
* * *
32893 GGTATATAAATGACAAAACATGTAAAGCGCTACCGAATATATTGAAA
66 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
* *
32940 GTGTCGATACTTTATAAAAATGTATCGATTCATAACAATATAACATGTAAAAAAATGACAAAACC
1 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACC
* * *
33005 GGTATATATATGACAAAACAGGTAAAGCGCTATCGGATATATTGAAA
66 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
* * *
33052 GTGTTGATACTTTATAAAAATGTATCGATCCATAAAAATATAACAGGTAAAAAAAATGACAATAC
1 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGT-AAAAAAATGACAAAAC
* *
33117 CGGTCTGTAAATGACAAAACAGGTAAAGCGCTACCGAATATATTGAAA
65 CGGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
* *
33165 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAATAGGT-AAAAAATGACAAAATC
1 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACC
33229 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
66 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
* * * * * *
33276 GTGTCGATACTTTAT-AAATTTTTTTGATCCATAACAATATAGCAGGTAAAAATATGACAAAACC
1 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACC
* * * *
33340 GGTCTATAAATAACAAAATAGGTAAAGCG--A---GATATATCGATA
66 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
33382 GTGTCGATACTTTAT
1 GTGTCGATACTTTAT
33397 TATAAGTATC
Statistics
Matches: 520, Mismatches: 47, Indels: 11
0.90 0.08 0.02
Matches are distributed among these distances:
106 25 0.05
109 1 0.00
110 26 0.05
111 115 0.22
112 205 0.39
113 148 0.28
ACGTcount: A:0.45, C:0.13, G:0.15, T:0.27
Consensus pattern (112 bp):
GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACC
GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
Found at i:33600 original size:182 final size:178
Alignment explanation
Indices: 33273--33722 Score: 602
Period size: 182 Copynumber: 2.5 Consensus size: 178
33263 GGATATATTG
* * * * * *
33273 AAAGTGTCGATACTTTAT-AAATTTTTTTGATCCATAACAATATAGCAGGTAAAAATATGACAAA
1 AAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAAGTAAAAATATGACAAA
** * ** *
33337 ACCGGTCTATAAATAACAAAATAGGT-AAAGCGAGATATATCGATAGTGTCGATACTTTATTATA
66 ACCGGTCTCGAAATGACAAAACCGGTAAAAGCGAGATATATCGAAAGTGTCGATACTTTATTATA
*
33401 AGTATCAGCAATTTTGGAATTTAAAAGAGAAA-AAGTTATAGCGCTAAT
131 AGTATCAGCAATTTTGGAATTTAAAAGA-AAAGAAGTTATAGCGCCAAT
* *
33449 AAAGTGTCGATACTTTATAAAAATGTATCGATCTATAATAATATAACAAGTAAAAATATGACAAA
1 AAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAAGTAAAAATATGACAAA
* * * *
33514 ACCGGTCTCGAAATGACAAAACCGGTAAAGAGCTACCGGATATGTTGAAAGTGTCGATATTTTAT
66 ACCGGTCTCGAAATGACAAAACCGGTAAA-AGCGA---GATATATCGAAAGTGTCGATACTTTAT
* *
33579 TATAAGTATC-GACACTTTTGGAATTTTAAAGAAAAGAAGTTATAGCGCCAAT
127 TATAAGTATCAG-CAATTTTGGAATTTAAAAGAAAAGAAGTTATAGCGCCAAT
* *
33631 AAAGTGTCGATACTTTATAAAAATGTATCAATCCATAACAATATAACATGTAAAAATATGACAAA
1 AAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAAGTAAAAATATGACAAA
*
33696 ATCGGTCTCGAAATGACAAAACCGGTA
66 ACCGGTCTCGAAATGACAAAACCGGTA
33723 GTAAAAAAGT
Statistics
Matches: 240, Mismatches: 26, Indels: 10
0.87 0.09 0.04
Matches are distributed among these distances:
176 18 0.08
177 59 0.25
178 2 0.01
179 4 0.02
181 4 0.02
182 153 0.64
ACGTcount: A:0.43, C:0.12, G:0.16, T:0.29
Consensus pattern (178 bp):
AAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAAGTAAAAATATGACAAA
ACCGGTCTCGAAATGACAAAACCGGTAAAAGCGAGATATATCGAAAGTGTCGATACTTTATTATA
AGTATCAGCAATTTTGGAATTTAAAAGAAAAGAAGTTATAGCGCCAAT
Found at i:37128 original size:23 final size:22
Alignment explanation
Indices: 37080--37128 Score: 55
Period size: 23 Copynumber: 2.2 Consensus size: 22
37070 TATTAGATAT
*
37080 TATTTTTTTTAATAAAACTACC
1 TATTTTTTTTAATAAAACTACA
*
37102 TATTTTTATTTACATAAAAGTA-A
1 TATTTTT-TTTA-ATAAAACTACA
37125 TATT
1 TATT
37129 ATCAATGTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
22 7 0.30
23 8 0.35
24 8 0.35
ACGTcount: A:0.39, C:0.08, G:0.02, T:0.51
Consensus pattern (22 bp):
TATTTTTTTTAATAAAACTACA
Found at i:38550 original size:84 final size:84
Alignment explanation
Indices: 38409--38571 Score: 218
Period size: 84 Copynumber: 1.9 Consensus size: 84
38399 TGGGGAAAGA
* * * **
38409 CAAGTGGGAGTACCAATTCAATTGGTGCATGAGAAGAAAAATTTAAATACCATTGTTTCGAATTC
1 CAAGTGGGAGTACCAATGCAAGTGGTGCATGAAAAGAAAAATGGAAATACCATTGTTTCGAATTC
*
38474 AACGATTGTGGAGAGATTG
66 AACAATTGTGGAGAGATTG
* * ** *
38493 CAAGTGGGAGTAGCAATGCCAGTGGTGCATGAAAAGAACGATGGAAATACCATTGTTTTGAATTC
1 CAAGTGGGAGTACCAATGCAAGTGGTGCATGAAAAGAAAAATGGAAATACCATTGTTTCGAATTC
*
38558 GACAATTGTGGAGA
66 AACAATTGTGGAGA
38572 AATTTCATGG
Statistics
Matches: 67, Mismatches: 12, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
84 67 1.00
ACGTcount: A:0.35, C:0.12, G:0.26, T:0.26
Consensus pattern (84 bp):
CAAGTGGGAGTACCAATGCAAGTGGTGCATGAAAAGAAAAATGGAAATACCATTGTTTCGAATTC
AACAATTGTGGAGAGATTG
Found at i:40824 original size:17 final size:16
Alignment explanation
Indices: 40802--40835 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
40792 TTAAAGGCTA
*
40802 TTTGTATTATTTCTCTC
1 TTTGTAATATTTC-CTC
40819 TTTGTAATATTTCCTC
1 TTTGTAATATTTCCTC
40835 T
1 T
40836 ATTAGTGAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.15, C:0.18, G:0.06, T:0.62
Consensus pattern (16 bp):
TTTGTAATATTTCCTC
Found at i:46360 original size:53 final size:55
Alignment explanation
Indices: 46286--46413 Score: 197
Period size: 53 Copynumber: 2.4 Consensus size: 55
46276 GGAGTATGGA
* * *
46286 ACTCGAATAATCTTTAACAATCGTGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
1 ACTCGAACAATCTTCAACAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
* *
46341 AC-C-CACAATCTTCATCAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
1 ACTCGAACAATCTTCAACAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
46394 ACTCGAACAATCTTCAACAA
1 ACTCGAACAATCTTCAACAA
46414 ATGGGTTCGC
Statistics
Matches: 64, Mismatches: 7, Indels: 4
0.85 0.09 0.05
Matches are distributed among these distances:
53 47 0.73
54 2 0.03
55 15 0.23
ACGTcount: A:0.30, C:0.28, G:0.12, T:0.29
Consensus pattern (55 bp):
ACTCGAACAATCTTCAACAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
Found at i:46538 original size:51 final size:51
Alignment explanation
Indices: 46375--47075 Score: 757
Period size: 51 Copynumber: 13.5 Consensus size: 51
46365 CTGCCCCCTA
* * * * *
46375 TTTCTTCAGAGAGTATA-AGACTCGAACAATCTTCAACAAATGGGTTCGCTCCCTA
1 TTTCTTTAGGGAGTATAGA-ACTCGAAC-ATCTT---CAAACGGGTTCGCTCCTTC
*
46430 TTTCTCTAGGGAGTATAGAACTCGAACATCTCTTCAAACGGGTTCGCTCCTTC
1 TTTCTTTAGGGAGTATAGAACTCGAACA--TCTTCAAACGGGTTCGCTCCTTC
* * *
46483 TTTCTTTAAGGAGTATAGAACTCGAACATCTTCAAACGGGTTCGTTCCTTT
1 TTTCTTTAGGGAGTATAGAACTCGAACATCTTCAAACGGGTTCGCTCCTTC
* *
46534 TTTCTTTAAGGAGTATAGAACTCGAACATCTTCAAACGGGTTCGCTCCCTC
1 TTTCTTTAGGGAGTATAGAACTCGAACATCTTCAAACGGGTTCGCTCCTTC
* *
46585 TTTCTTTAGGGAGTATAGAACTCGAACATCTCTTC--ACGGGTTTGCTCCCTC
1 TTTCTTTAGGGAGTATAGAACTCGAACA--TCTTCAAACGGGTTCGCTCCTTC
* * *
46636 TTTCTCTAGGGAGTATGGAACTCGAACATCTTCAAACGGGTTCGCTCATTC
1 TTTCTTTAGGGAGTATAGAACTCGAACATCTTCAAACGGGTTCGCTCCTTC
* * * * * *
46687 TTTCATTAAGGAGTATGGAACTC-AGATATCTTCACACGGGTTCGCTCCCTC
1 TTTCTTTAGGGAGTATAGAACTCGA-ACATCTTCAAACGGGTTCGCTCCTTC
* *
46738 TTTCTCTAGGGAGTATGGAACTC-AGACATCTCTTCAAACGGGTTCGCTCCTTC
1 TTTCTTTAGGGAGTATAGAACTCGA-ACA--TCTTCAAACGGGTTCGCTCCTTC
* * * * **
46791 TTTCTTTAAGGAGTATAGAACTCGCATATCTTCACACGGGTTCGCTCCCGC
1 TTTCTTTAGGGAGTATAGAACTCGAACATCTTCAAACGGGTTCGCTCCTTC
* * *
46842 TTTCTCTAGGGAGTATGGAACTC-AGACATCTCTTCAAATGGGTTCGCTCCTTC
1 TTTCTTTAGGGAGTATAGAACTCGA-ACA--TCTTCAAACGGGTTCGCTCCTTC
** * *
46895 TTTCTTTAAAGAGTATGGAACTCGAACATCTTTAAACGGGTTCGCTCCTTC
1 TTTCTTTAGGGAGTATAGAACTCGAACATCTTCAAACGGGTTCGCTCCTTC
* * * * *
46946 TTTCTTTAAGGAAGTATAGAACTTGAATGATCTTCTGAAAACGGGTTCTCTCCCTC
1 TTTCTTT-AGGGAGTATAGAACTCGAA-CATCTTC---AAACGGGTTCGCTCCTTC
* *
47002 TTTCTTCAGGGAGTATAGAACTCGAAAATCTTCAAACGGGTTCGCTCCTTC
1 TTTCTTTAGGGAGTATAGAACTCGAACATCTTCAAACGGGTTCGCTCCTTC
* *
47053 TTTCTCTAGGGAGTATGGAACTC
1 TTTCTTTAGGGAGTATAGAACTC
47076 AAATAATCTT
Statistics
Matches: 553, Mismatches: 73, Indels: 44
0.83 0.11 0.07
Matches are distributed among these distances:
49 5 0.01
50 1 0.00
51 322 0.58
52 14 0.03
53 137 0.25
54 8 0.01
55 39 0.07
56 27 0.05
ACGTcount: A:0.24, C:0.24, G:0.19, T:0.33
Consensus pattern (51 bp):
TTTCTTTAGGGAGTATAGAACTCGAACATCTTCAAACGGGTTCGCTCCTTC
Found at i:46556 original size:104 final size:104
Alignment explanation
Indices: 46385--47075 Score: 844
Period size: 104 Copynumber: 6.6 Consensus size: 104
46375 TTTCTTCAGA
* * *
46385 GAGTATA-AGACTCGAACAATCTTCAACAAATGGGTTCGCTCCCTATTTCTCTAGGGAGTATAGA
1 GAGTATAGA-ACTCGAAC-ATCTT---CAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGA
46449 ACTCGAACATCTCTTCAAACGGGTTCGCTCCTTCTTTCTTTAAG
61 ACTCGAACATCTCTTCAAACGGGTTCGCTCCTTCTTTCTTTAAG
* * * * * *
46493 GAGTATAGAACTCGAACATCTTCAAACGGGTTCGTTCCTTTTTTCTTTAAGGAGTATAGAACTCG
1 GAGTATAGAACTCGAACATCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTCG
* *
46558 AACA--TCTTCAAACGGGTTCGCTCCCTCTTTCTTTAGG
66 AACATCTCTTCAAACGGGTTCGCTCCTTCTTTCTTTAAG
*
46595 GAGTATAGAACTCGAACATCTCTTC--ACGGGTTTGCTCCCTCTTTCTCTAGGGAGTATGGAACT
1 GAGTATAGAACTCGAACA--TCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACT
* *
46658 CGAACA--TCTTCAAACGGGTTCGCTCATTCTTTCATTAAG
64 CGAACATCTCTTCAAACGGGTTCGCTCCTTCTTTCTTTAAG
* * *
46697 GAGTATGGAACTC-AGATATCTTCACACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTC
1 GAGTATAGAACTCGA-ACATCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTC
46761 -AGACATCTCTTCAAACGGGTTCGCTCCTTCTTTCTTTAAG
65 GA-ACATCTCTTCAAACGGGTTCGCTCCTTCTTTCTTTAAG
* * * *
46801 GAGTATAGAACTCGCATATCTTCACACGGGTTCGCTCCCGCTTTCTCTAGGGAGTATGGAACTC-
1 GAGTATAGAACTCGAACATCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTCG
* *
46865 AGACATCTCTTCAAATGGGTTCGCTCCTTCTTTCTTTAAA
66 A-ACATCTCTTCAAACGGGTTCGCTCCTTCTTTCTTTAAG
* * * * * * *
46905 GAGTATGGAACTCGAACATCTTTAAACGGGTTCGCTCCTTCTTTCTTTAAGGAAGTATAGAACTT
1 GAGTATAGAACTCGAACATCTTCAAACGGGTTCGCTCCCTCTTTCTCT-AGGGAGTATGGAACTC
* ** * * * *
46970 GAATGATCTTCTGAAAACGGGTTCTCTCCCTCTTTCTTCAGG
65 GAA-CATC-TCTTCAAACGGGTTCGCTCCTTCTTTCTTTAAG
* *
47012 GAGTATAGAACTCGAAAATCTTCAAACGGGTTCGCTCCTTCTTTCTCTAGGGAGTATGGAACTC
1 GAGTATAGAACTCGAACATCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTC
47076 AAATAATCTT
Statistics
Matches: 513, Mismatches: 56, Indels: 30
0.86 0.09 0.05
Matches are distributed among these distances:
100 5 0.01
101 2 0.00
102 170 0.33
104 215 0.42
105 14 0.03
106 17 0.03
107 74 0.14
108 15 0.03
109 1 0.00
ACGTcount: A:0.24, C:0.24, G:0.19, T:0.33
Consensus pattern (104 bp):
GAGTATAGAACTCGAACATCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTCG
AACATCTCTTCAAACGGGTTCGCTCCTTCTTTCTTTAAG
Found at i:47529 original size:36 final size:36
Alignment explanation
Indices: 47457--47654 Score: 238
Period size: 36 Copynumber: 5.5 Consensus size: 36
47447 ACTCTTCTGA
* * *
47457 GAAGGCTTAAAATGGATCTGCTTCACTACTT-T-TGGT
1 GAAGGCTTAAGATGG-TTTGCTTCACTA-TTCTCCGGT
* * * *
47493 GAAGACTTAAGATGCTTTGCTTCACTACTCTCTGGT
1 GAAGGCTTAAGATGGTTTGCTTCACTATTCTCCGGT
* *
47529 GAAGACTTATGATGGTTTGCTTCACTATTCTCCGGT
1 GAAGGCTTAAGATGGTTTGCTTCACTATTCTCCGGT
* * *
47565 GAAGGCTTCAGATTGATTGCTTCACTATTCTCCGGT
1 GAAGGCTTAAGATGGTTTGCTTCACTATTCTCCGGT
*
47601 GAAGGCTTCAGATGGTTTGCTTCACTATTCTCCGGT
1 GAAGGCTTAAGATGGTTTGCTTCACTATTCTCCGGT
*
47637 GAAGGCTTAGGATGGTTT
1 GAAGGCTTAAGATGGTTT
47655 TTCTCCAATC
Statistics
Matches: 142, Mismatches: 18, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
34 1 0.01
35 12 0.08
36 129 0.91
ACGTcount: A:0.21, C:0.19, G:0.24, T:0.36
Consensus pattern (36 bp):
GAAGGCTTAAGATGGTTTGCTTCACTATTCTCCGGT
Found at i:49050 original size:125 final size:124
Alignment explanation
Indices: 48829--49080 Score: 353
Period size: 125 Copynumber: 2.0 Consensus size: 124
48819 ACTAATGTCG
* * * *
48829 CAACATTATTTTATTCTGGTACGGGCCTTCAAATGCCTCAATATCTCAAATTATAAGGCTCATTC
1 CAACATTATCTCATACTGGTACGGGCCTTCAAATGCCTCAATACCTCAAATTATAAGGCTCATTC
** * *
48894 TCAATGCCTTCTTGGTCTGAATCTTGTCATTTCATCATGATGTGGGTTCAGTCGCGCCC
66 TCAATGCCTTCTTGGTCTGAATCTTGTCATTTCAAAATGATGGGGGTTCAATCGCGCCC
* *
48953 CAACATTATCTCATACTGGTACGGGCCTTCAAAATGCC-CCATCACCTCAAATTGTAAGGCTCAT
1 CAACATTATCTCATACTGGTACGGGCCTTC-AAATGCCTCAAT-ACCTCAAATTATAAGGCTCAT
** * *
49017 TCTTGATGCCTTCTTTGTCTGAATCTTGTCATTTCAAAATGATGGGGGTTCAATCGTGCCC
64 TCTCAATGCCTTCTTGGTCTGAATCTTGTCATTTCAAAATGATGGGGGTTCAATCGCGCCC
49078 CAA
1 CAA
49081 TGTGGGTATT
Statistics
Matches: 112, Mismatches: 14, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
124 30 0.27
125 82 0.73
ACGTcount: A:0.24, C:0.25, G:0.17, T:0.34
Consensus pattern (124 bp):
CAACATTATCTCATACTGGTACGGGCCTTCAAATGCCTCAATACCTCAAATTATAAGGCTCATTC
TCAATGCCTTCTTGGTCTGAATCTTGTCATTTCAAAATGATGGGGGTTCAATCGCGCCC
Found at i:60151 original size:17 final size:16
Alignment explanation
Indices: 60129--60162 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
60119 TTAAAGACTA
*
60129 TTTGTATTATTTCTCTC
1 TTTGTAATATTTC-CTC
60146 TTTGTAATATTTCCTC
1 TTTGTAATATTTCCTC
60162 T
1 T
60163 ATTAGTGAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.15, C:0.18, G:0.06, T:0.62
Consensus pattern (16 bp):
TTTGTAATATTTCCTC
Found at i:68046 original size:145 final size:145
Alignment explanation
Indices: 67778--68071 Score: 552
Period size: 145 Copynumber: 2.0 Consensus size: 145
67768 TTTTTGACGA
*
67778 AAATCTATTTTAAAGTTCTACGTATTAATATTCCGATATCTTTCAATGACTGTCCAATGAGACTA
1 AAATATATTTTAAAGTTCTACGTATTAATATTCCGATATCTTTCAATGACTGTCCAATGAGACTA
67843 ATTTTGAGGTAGGTTGTTCGTCTTCTCGAAATAATGCTTTTAACCATTTAGATTTTTTAATAAAC
66 ATTTTGAGGTAGGTTGTTCGTCTTCTCGAAATAATGCTTTTAACCATTTAGATTTTTTAATAAAC
67908 ACCCCCAAATCCCAT
131 ACCCCCAAATCCCAT
*
67923 AAATATATTTTAAAGTTCTACGTATTAATATTCCGATATCTTTCAATGACTGTCCAATGAGGCTA
1 AAATATATTTTAAAGTTCTACGTATTAATATTCCGATATCTTTCAATGACTGTCCAATGAGACTA
* *
67988 ATTTTGAGGTAGGTTGTTCGTCTTCTCGAAATAATGCTTTTCACTATTTAGATTTTTTAATAAAC
66 ATTTTGAGGTAGGTTGTTCGTCTTCTCGAAATAATGCTTTTAACCATTTAGATTTTTTAATAAAC
68053 ACCCCCAAATCCCAT
131 ACCCCCAAATCCCAT
68068 AAAT
1 AAAT
68072 CTAAGAAAGT
Statistics
Matches: 145, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
145 145 1.00
ACGTcount: A:0.31, C:0.18, G:0.12, T:0.39
Consensus pattern (145 bp):
AAATATATTTTAAAGTTCTACGTATTAATATTCCGATATCTTTCAATGACTGTCCAATGAGACTA
ATTTTGAGGTAGGTTGTTCGTCTTCTCGAAATAATGCTTTTAACCATTTAGATTTTTTAATAAAC
ACCCCCAAATCCCAT
Found at i:69041 original size:31 final size:30
Alignment explanation
Indices: 68991--69110 Score: 98
Period size: 30 Copynumber: 4.0 Consensus size: 30
68981 TTCAACAGTC
* * *
68991 AAATTGGTA-TTTATTTAAAGTTTAAGAGTT
1 AAATTAGTATTTTATCTAAAGTTTAAG-GTA
*
69021 AAATTAGTATTTTATCTAAAGTGTAAGGTA
1 AAATTAGTATTTTATCTAAAGTTTAAGGTA
* * * * *
69051 AAATTAGCATTTTAACCAAAGTTTAGGGTC
1 AAATTAGTATTTTATCTAAAGTTTAAGGTA
* * * *
69081 CAATTAGCATTCTATCTAAAATTTAGAGGT
1 AAATTAGTATTTTATCTAAAGTTTA-AGGT
69111 GAACTTAAAA
Statistics
Matches: 72, Mismatches: 16, Indels: 3
0.79 0.18 0.03
Matches are distributed among these distances:
30 54 0.75
31 18 0.25
ACGTcount: A:0.38, C:0.07, G:0.16, T:0.39
Consensus pattern (30 bp):
AAATTAGTATTTTATCTAAAGTTTAAGGTA
Found at i:80982 original size:2 final size:2
Alignment explanation
Indices: 80932--80962 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
80922 AATTAAATAC
*
80932 GA GA GA GA GA CA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
80963 TCTTGCGAAG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.03, G:0.48, T:0.00
Consensus pattern (2 bp):
GA
Done.